Proteome Informatics Group > Java Proteomic Library



This application generates decoy sequences.


usage: FastaDecoy <Fasta> [-a] [-d <arg>] [-e <arg>] [-f <arg>] [-h] 
[-i <arg>] [-k <arg>] [-l <arg>] [-m <arg>] [-o <arg>] [-p <arg>] [-q] [-s <arg>] [-t <arg>] [-v]

 -a,--append                combine decoy and original in one result file
                            by default: true.
 -d,--decoyFlag <arg>       decoy flag
                            by default: DECOY_.
 -e,--enzymes <arg>         define enzyme that digest proteins separately with:
                            enzyme name among 'Caspase-1, Caspase-10, Glu-C_bicarbonate, Caspase-3,
                            Thermolysine, Lys-C, Pepsin_pH1.3, Caspase-8, Glu-C_phosphate, Caspase-9,
                            Caspase-5, CNBr, ChymoTrypsin_lowspec, Trypsin, ChymoTrypsin_FYL,
                            Proteinase-K, Caspase-7, Pepsin_pHgt2, ChymoTrypsin_highspec,
                            BNPS-Skatole, Enterokinase, Caspase-6, Arg-C, Asp-N, ChymoTrypsin_FYLW,
                            Caspase-4, Caspase-2'.
                            or custom motifs respecting the following grammar:
                            <pre-cut> <cut-token>
                            <cut-token> := '|'
                            <pre-cut> := (<AA> or <AA-class>)+
                            <post-cut> := (<AA> or <AA-class>)+
                            <AA> := [A-Z]
                            <AA-class> := '[' AA+ ']'
                            by default: Trypsin.
 -f,--fastaFormat <arg>     Format of fasta header. Either simple ">P00001" sp (SwissProt) ipi (IPI)
                            or user defined with the following syntax:
                            regexp: regular expression to identify header
                            separator: char that separates header entries
                            index: index of protein name in list of header entries 		 
                            example (SwissProt header): "^sp\|.+$"@|@1by default: simple.
 -h,--help                  print this message.
 -i,--setting-file <arg>    give a property file with all input settings.
 -k,--keepTerm <arg>        Keep terminus of shuffled peptides
                            (peptideShuffle method only). Either
                            cterm (keep C-Terminus)
                            nterm (keep N-Terminus)
                            none (do not keep termini)
                            by default: cterm.
 -l,--length <arg>          don't shuffle peptides shorter than : 5.
 -m,--method <arg>          method for decoy sequence generation. Either
                            peptideShuffle (random permutation of peptide sequence leaving C-term)
                            proteinShuffle (random permutation of protein sequence)	
                            proteinReverse (reverse protein sequence)
                            by default: peptShuffle.
 -o,--output <arg>          set the output filename
 -p,--decoyFlagPos <arg>    where to insert decoy flag
                            beforeID: before protein id
                            startHead: beginning of header line (after '>' sign)
	                        startHead&beforeID : both of the above
                            by default: beforeID.
 -q,--quiet                 quiet mode (verbose off)
                            by default: false.
 -s,--simThreshold <arg>    maximal similarity between shuffled und
                            original peptide spectrum : 0.0.
 -t,--shuffleTrials <arg>   maximal number of peptide shuffling trials : 10.
 -v,--version               print the version info.



The latest version is v1.0 - Download app.